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45 #include "gromacs/utility/smalloc.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/fileio/xvgr.h"
52 #include "gromacs/utility/futil.h"
53 #include "gromacs/commandline/pargs.h"
55 #include "gromacs/fileio/tpxio.h"
56 #include "gromacs/fileio/trxio.h"
57 #include "gromacs/fileio/confio.h"
61 #include "gromacs/utility/fatalerror.h"
63 /****************************************************************************/
64 /* This program calculates the order parameter per atom for an interface or */
65 /* bilayer, averaged over time. */
66 /* S = 1/2 * (3 * cos(i)cos(j) - delta(ij)) */
67 /* It is assumed that the order parameter with respect to a box-axis */
68 /* is calculated. In that case i = j = axis, and delta(ij) = 1. */
70 /* Peter Tieleman, April 1995 */
71 /* P.J. van Maaren, November 2005 Added tetrahedral stuff */
72 /****************************************************************************/
74 static void find_nearest_neighbours(int ePBC,
75 int natoms, matrix box,
76 rvec x[], int maxidx, atom_id index[],
77 real *sgmean, real *skmean,
78 int nslice, int slice_dim,
79 real sgslice[], real skslice[],
84 int ix, jx, nsgbin, *sgbin;
85 int i1, i2, i, ibin, j, k, l, n, *nn[4];
86 rvec dx, dx1, dx2, rj, rk, urk, urj;
87 real cost, cost2, *sgmol, *skmol, rmean, rmean2, r2, box2, *r_nn[4];
93 real onethird = 1.0/3.0;
94 /* dmat = init_mat(maxidx, FALSE); */
95 box2 = box[XX][XX] * box[XX][XX];
96 snew(sl_count, nslice);
97 for (i = 0; (i < 4); i++)
99 snew(r_nn[i], natoms);
102 for (j = 0; (j < natoms); j++)
111 /* Must init pbc every step because of pressure coupling */
112 set_pbc(&pbc, ePBC, box);
114 gmx_rmpbc(gpbc, natoms, box, x);
116 nsgbin = 1 + 1/0.0005;
122 for (i = 0; (i < maxidx); i++) /* loop over index file */
125 for (j = 0; (j < maxidx); j++)
134 pbc_dx(&pbc, x[ix], x[jx], dx);
137 /* set_mat_entry(dmat,i,j,r2); */
139 /* determine the nearest neighbours */
142 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
143 r_nn[2][i] = r_nn[1][i]; nn[2][i] = nn[1][i];
144 r_nn[1][i] = r_nn[0][i]; nn[1][i] = nn[0][i];
145 r_nn[0][i] = r2; nn[0][i] = j;
147 else if (r2 < r_nn[1][i])
149 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
150 r_nn[2][i] = r_nn[1][i]; nn[2][i] = nn[1][i];
151 r_nn[1][i] = r2; nn[1][i] = j;
153 else if (r2 < r_nn[2][i])
155 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
156 r_nn[2][i] = r2; nn[2][i] = j;
158 else if (r2 < r_nn[3][i])
160 r_nn[3][i] = r2; nn[3][i] = j;
165 /* calculate mean distance between nearest neighbours */
167 for (j = 0; (j < 4); j++)
169 r_nn[j][i] = sqrt(r_nn[j][i]);
178 /* Chau1998a eqn 3 */
179 /* angular part tetrahedrality order parameter per atom */
180 for (j = 0; (j < 3); j++)
182 for (k = j+1; (k < 4); k++)
184 pbc_dx(&pbc, x[ix], x[index[nn[k][i]]], rk);
185 pbc_dx(&pbc, x[ix], x[index[nn[j][i]]], rj);
190 cost = iprod(urk, urj) + onethird;
193 /* sgmol[i] += 3*cost2/32; */
196 /* determine distribution */
197 ibin = nsgbin * cost2;
202 /* printf("%d %d %f %d %d\n", j, k, cost * cost, ibin, sgbin[ibin]);*/
208 /* normalize sgmol between 0.0 and 1.0 */
209 sgmol[i] = 3*sgmol[i]/32;
212 /* distance part tetrahedrality order parameter per atom */
213 rmean2 = 4 * 3 * rmean * rmean;
214 for (j = 0; (j < 4); j++)
216 skmol[i] += (rmean - r_nn[j][i]) * (rmean - r_nn[j][i]) / rmean2;
217 /* printf("%d %f (%f %f %f %f) \n",
218 i, skmol[i], rmean, rmean2, r_nn[j][i], (rmean - r_nn[j][i]) );
224 /* Compute sliced stuff */
225 sl_index = gmx_nint((1+x[i][slice_dim]/box[slice_dim][slice_dim])*nslice) % nslice;
226 sgslice[sl_index] += sgmol[i];
227 skslice[sl_index] += skmol[i];
228 sl_count[sl_index]++;
229 } /* loop over entries in index file */
234 for (i = 0; (i < nslice); i++)
238 sgslice[i] /= sl_count[i];
239 skslice[i] /= sl_count[i];
246 for (i = 0; (i < 4); i++)
254 static void calc_tetra_order_parm(const char *fnNDX, const char *fnTPS,
255 const char *fnTRX, const char *sgfn,
257 int nslice, int slice_dim,
258 const char *sgslfn, const char *skslfn,
259 const output_env_t oenv)
261 FILE *fpsg = NULL, *fpsk = NULL;
264 char title[STRLEN], fn[STRLEN], subtitle[STRLEN];
273 int i, *isize, ng, nframes;
274 real *sg_slice, *sg_slice_tot, *sk_slice, *sk_slice_tot;
275 gmx_rmpbc_t gpbc = NULL;
278 read_tps_conf(fnTPS, title, &top, &ePBC, &xtop, NULL, box, FALSE);
280 snew(sg_slice, nslice);
281 snew(sk_slice, nslice);
282 snew(sg_slice_tot, nslice);
283 snew(sk_slice_tot, nslice);
285 /* get index groups */
286 printf("Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation:\n");
290 get_index(&top.atoms, fnNDX, ng, isize, index, grpname);
292 /* Analyze trajectory */
293 natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
294 if (natoms > top.atoms.nr)
296 gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
297 top.atoms.nr, natoms);
299 check_index(NULL, ng, index[0], NULL, natoms);
301 fpsg = xvgropen(sgfn, "S\\sg\\N Angle Order Parameter", "Time (ps)", "S\\sg\\N",
303 fpsk = xvgropen(skfn, "S\\sk\\N Distance Order Parameter", "Time (ps)", "S\\sk\\N",
306 /* loop over frames */
307 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
311 find_nearest_neighbours(ePBC, natoms, box, x, isize[0], index[0],
312 &sg, &sk, nslice, slice_dim, sg_slice, sk_slice, gpbc);
313 for (i = 0; (i < nslice); i++)
315 sg_slice_tot[i] += sg_slice[i];
316 sk_slice_tot[i] += sk_slice[i];
318 fprintf(fpsg, "%f %f\n", t, sg);
319 fprintf(fpsk, "%f %f\n", t, sk);
322 while (read_next_x(oenv, status, &t, x, box));
324 gmx_rmpbc_done(gpbc);
333 fpsg = xvgropen(sgslfn,
334 "S\\sg\\N Angle Order Parameter / Slab", "(nm)", "S\\sg\\N",
336 fpsk = xvgropen(skslfn,
337 "S\\sk\\N Distance Order Parameter / Slab", "(nm)", "S\\sk\\N",
339 for (i = 0; (i < nslice); i++)
341 fprintf(fpsg, "%10g %10g\n", (i+0.5)*box[slice_dim][slice_dim]/nslice,
342 sg_slice_tot[i]/nframes);
343 fprintf(fpsk, "%10g %10g\n", (i+0.5)*box[slice_dim][slice_dim]/nslice,
344 sk_slice_tot[i]/nframes);
351 /* Print name of first atom in all groups in index file */
352 static void print_types(atom_id index[], atom_id a[], int ngrps,
353 char *groups[], t_topology *top)
357 fprintf(stderr, "Using following groups: \n");
358 for (i = 0; i < ngrps; i++)
360 fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %d\n",
361 groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
363 fprintf(stderr, "\n");
366 static void check_length(real length, int a, int b)
370 fprintf(stderr, "WARNING: distance between atoms %d and "
371 "%d > 0.3 nm (%f). Index file might be corrupt.\n",
376 void calc_order(const char *fn, atom_id *index, atom_id *a, rvec **order,
377 real ***slOrder, real *slWidth, int nslices, gmx_bool bSliced,
378 gmx_bool bUnsat, t_topology *top, int ePBC, int ngrps, int axis,
379 gmx_bool permolecule, gmx_bool radial, gmx_bool distcalc, const char *radfn,
381 const output_env_t oenv)
383 /* if permolecule = TRUE, order parameters will be calculed per molecule
384 * and stored in slOrder with #slices = # molecules */
385 rvec *x0, /* coordinates with pbc */
386 *x1, /* coordinates without pbc */
387 dist; /* vector between two atoms */
388 matrix box; /* box (3x3) */
390 rvec cossum, /* sum of vector angles for three axes */
391 Sx, Sy, Sz, /* the three molecular axes */
392 tmp1, tmp2, /* temp. rvecs for calculating dot products */
393 frameorder; /* order parameters for one frame */
394 real *slFrameorder; /* order parameter for one frame, per slice */
395 real length, /* total distance between two atoms */
396 t, /* time from trajectory */
397 z_ave, z1, z2; /* average z, used to det. which slice atom is in */
398 int natoms, /* nr. atoms in trj */
399 nr_tails, /* nr tails, to check if index file is correct */
400 size = 0, /* nr. of atoms in group. same as nr_tails */
401 i, j, m, k, l, teller = 0,
402 slice, /* current slice number */
404 int *slCount; /* nr. of atoms in one slice */
405 real dbangle = 0, /* angle between double bond and axis */
406 sdbangle = 0; /* sum of these angles */
407 gmx_bool use_unitvector = FALSE; /* use a specified unit vector instead of axis to specify unit normal*/
408 rvec direction, com, dref, dvec;
409 int comsize, distsize;
410 atom_id *comidx = NULL, *distidx = NULL;
411 char *grpname = NULL;
413 real arcdist, tmpdist;
414 gmx_rmpbc_t gpbc = NULL;
416 /* PBC added for center-of-mass vector*/
417 /* Initiate the pbc structure */
418 memset(&pbc, 0, sizeof(pbc));
420 if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
422 gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
425 nr_tails = index[1] - index[0];
426 fprintf(stderr, "Number of elements in first group: %d\n", nr_tails);
427 /* take first group as standard. Not rocksolid, but might catch error in index*/
432 bSliced = FALSE; /*force slices off */
433 fprintf(stderr, "Calculating order parameters for each of %d molecules\n",
439 use_unitvector = TRUE;
440 fprintf(stderr, "Select an index group to calculate the radial membrane normal\n");
441 get_index(&top->atoms, radfn, 1, &comsize, &comidx, &grpname);
449 fprintf(stderr, "Select an index group to use as distance reference\n");
450 get_index(&top->atoms, radfn, 1, &distsize, &distidx, &grpname);
451 bSliced = FALSE; /*force slices off*/
454 if (use_unitvector && bSliced)
456 fprintf(stderr, "Warning: slicing and specified unit vectors are not currently compatible\n");
459 snew(slCount, nslices);
460 snew(*slOrder, nslices);
461 for (i = 0; i < nslices; i++)
463 snew((*slOrder)[i], ngrps);
467 snew(*distvals, nslices);
468 for (i = 0; i < nslices; i++)
470 snew((*distvals)[i], ngrps);
474 snew(slFrameorder, nslices);
479 *slWidth = box[axis][axis]/nslices;
480 fprintf(stderr, "Box divided in %d slices. Initial width of slice: %f\n",
486 nr_tails = index[1] - index[0];
487 fprintf(stderr, "Number of elements in first group: %d\n", nr_tails);
488 /* take first group as standard. Not rocksolid, but might catch error
494 gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
495 /*********** Start processing trajectory ***********/
500 *slWidth = box[axis][axis]/nslices;
504 set_pbc(&pbc, ePBC, box);
505 gmx_rmpbc_copy(gpbc, natoms, box, x0, x1);
507 /* Now loop over all groups. There are ngrps groups, the order parameter can
508 be calculated for grp 1 to grp ngrps - 1. For each group, loop over all
509 atoms in group, which is index[i] to (index[i+1] - 1) See block.h. Of
510 course, in this case index[i+1] -index[i] has to be the same for all
511 groups, namely the number of tails. i just runs over all atoms in a tail,
512 so for DPPC ngrps = 16 and i runs from 1 to 14, including 14
518 /*center-of-mass determination*/
519 com[XX] = 0.0; com[YY] = 0.0; com[ZZ] = 0.0;
520 for (j = 0; j < comsize; j++)
522 rvec_inc(com, x1[comidx[j]]);
524 svmul(1.0/comsize, com, com);
528 dref[XX] = 0.0; dref[YY] = 0.0; dref[ZZ] = 0.0;
529 for (j = 0; j < distsize; j++)
531 rvec_inc(dist, x1[distidx[j]]);
533 svmul(1.0/distsize, dref, dref);
536 pbc_dx(&pbc, dref, com, dvec);
541 for (i = 1; i < ngrps - 1; i++)
543 clear_rvec(frameorder);
545 size = index[i+1] - index[i];
546 if (size != nr_tails)
548 gmx_fatal(FARGS, "grp %d does not have same number of"
549 " elements as grp 1\n", i);
552 for (j = 0; j < size; j++)
555 /*create unit vector*/
557 pbc_dx(&pbc, x1[a[index[i]+j]], com, direction);
558 unitv(direction, direction);
561 fprintf(stderr,"X %f %f %f\tcom %f %f %f\tdirection %f %f %f\n",x1[a[index[i]+j]][0],x1[a[index[i]+j]][1],x1[a[index[i]+j]][2],com[0],com[1],com[2],
562 direction[0],direction[1],direction[2]);*/
567 /* Using convention for unsaturated carbons */
568 /* first get Sz, the vector from Cn to Cn+1 */
569 rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i]+j]], dist);
571 check_length(length, a[index[i]+j], a[index[i+1]+j]);
572 svmul(1/length, dist, Sz);
574 /* this is actually the cosine of the angle between the double bond
575 and axis, because Sz is normalized and the two other components of
576 the axis on the bilayer are zero */
579 sdbangle += gmx_angle(direction, Sz); /*this can probably be optimized*/
583 sdbangle += acos(Sz[axis]);
588 /* get vector dist(Cn-1,Cn+1) for tail atoms */
589 rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i-1]+j]], dist);
590 length = norm(dist); /* determine distance between two atoms */
591 check_length(length, a[index[i-1]+j], a[index[i+1]+j]);
593 svmul(1/length, dist, Sz);
594 /* Sz is now the molecular axis Sz, normalized and all that */
597 /* now get Sx. Sx is normal to the plane of Cn-1, Cn and Cn+1 so
598 we can use the outer product of Cn-1->Cn and Cn+1->Cn, I hope */
599 rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i]+j]], tmp1);
600 rvec_sub(x1[a[index[i-1]+j]], x1[a[index[i]+j]], tmp2);
601 cprod(tmp1, tmp2, Sx);
602 svmul(1/norm(Sx), Sx, Sx);
604 /* now we can get Sy from the outer product of Sx and Sz */
606 svmul(1/norm(Sy), Sy, Sy);
608 /* the square of cosine of the angle between dist and the axis.
609 Using the innerproduct, but two of the three elements are zero
610 Determine the sum of the orderparameter of all atoms in group
614 cossum[XX] = sqr(iprod(Sx, direction)); /* this is allowed, since Sa is normalized */
615 cossum[YY] = sqr(iprod(Sy, direction));
616 cossum[ZZ] = sqr(iprod(Sz, direction));
620 cossum[XX] = sqr(Sx[axis]); /* this is allowed, since Sa is normalized */
621 cossum[YY] = sqr(Sy[axis]);
622 cossum[ZZ] = sqr(Sz[axis]);
625 for (m = 0; m < DIM; m++)
627 frameorder[m] += 0.5 * (3 * cossum[m] - 1);
632 /* get average coordinate in box length for slicing,
633 determine which slice atom is in, increase count for that
634 slice. slFrameorder and slOrder are reals, not
635 rvecs. Only the component [axis] of the order tensor is
636 kept, until I find it necessary to know the others too
639 z1 = x1[a[index[i-1]+j]][axis];
640 z2 = x1[a[index[i+1]+j]][axis];
641 z_ave = 0.5 * (z1 + z2);
644 z_ave += box[axis][axis];
646 if (z_ave > box[axis][axis])
648 z_ave -= box[axis][axis];
651 slice = (int)(0.5 + (z_ave / (*slWidth))) - 1;
652 slCount[slice]++; /* determine slice, increase count */
654 slFrameorder[slice] += 0.5 * (3 * cossum[axis] - 1);
656 else if (permolecule)
658 /* store per-molecule order parameter
659 * To just track single-axis order: (*slOrder)[j][i] += 0.5 * (3 * iprod(cossum,direction) - 1);
660 * following is for Scd order: */
661 (*slOrder)[j][i] += -1* (0.3333 * (3 * cossum[XX] - 1) + 0.3333 * 0.5 * (3 * cossum[YY] - 1));
667 /* bin order parameter by arc distance from reference group*/
668 arcdist = gmx_angle(dvec, direction);
669 (*distvals)[j][i] += arcdist;
673 /* Want minimum lateral distance to first group calculated */
674 tmpdist = trace(box); /* should be max value */
675 for (k = 0; k < distsize; k++)
677 pbc_dx(&pbc, x1[distidx[k]], x1[a[index[i]+j]], dvec);
678 /* at the moment, just remove dvec[axis] */
680 tmpdist = min(tmpdist, norm2(dvec));
682 //fprintf(stderr, "Min dist %f; trace %f\n", tmpdist, trace(box));
683 (*distvals)[j][i] += sqrt(tmpdist);
686 } /* end loop j, over all atoms in group */
688 for (m = 0; m < DIM; m++)
690 (*order)[i][m] += (frameorder[m]/size);
694 { /*Skip following if doing per-molecule*/
695 for (k = 0; k < nslices; k++)
697 if (slCount[k]) /* if no elements, nothing has to be added */
699 (*slOrder)[k][i] += slFrameorder[k]/slCount[k];
700 slFrameorder[k] = 0; slCount[k] = 0;
703 } /* end loop i, over all groups in indexfile */
708 while (read_next_x(oenv, status, &t, x0, box));
709 /*********** done with status file **********/
711 fprintf(stderr, "\nRead trajectory. Printing parameters to file\n");
712 gmx_rmpbc_done(gpbc);
714 /* average over frames */
715 for (i = 1; i < ngrps - 1; i++)
717 svmul(1.0/nr_frames, (*order)[i], (*order)[i]);
718 fprintf(stderr, "Atom %d Tensor: x=%g , y=%g, z=%g\n", i, (*order)[i][XX],
719 (*order)[i][YY], (*order)[i][ZZ]);
720 if (bSliced || permolecule)
722 for (k = 0; k < nslices; k++)
724 (*slOrder)[k][i] /= nr_frames;
729 for (k = 0; k < nslices; k++)
731 (*distvals)[k][i] /= nr_frames;
738 fprintf(stderr, "Average angle between double bond and normal: %f\n",
739 180*sdbangle/(nr_frames * size*M_PI));
742 sfree(x0); /* free memory used by coordinate arrays */
759 void order_plot(rvec order[], real *slOrder[], const char *afile, const char *bfile,
760 const char *cfile, int ngrps, int nslices, real slWidth, gmx_bool bSzonly,
761 gmx_bool permolecule, real **distvals, const output_env_t oenv)
763 FILE *ord, *slOrd; /* xvgr files with order parameters */
764 int atom, slice; /* atom corresponding to order para.*/
765 char buf[256]; /* for xvgr title */
766 real S; /* order parameter averaged over all atoms */
770 sprintf(buf, "Scd order parameters");
771 ord = xvgropen(afile, buf, "Atom", "S", oenv);
772 sprintf(buf, "Orderparameters per atom per slice");
773 slOrd = xvgropen(bfile, buf, "Molecule", "S", oenv);
774 for (atom = 1; atom < ngrps - 1; atom++)
776 fprintf(ord, "%12d %12g\n", atom, -1 * (0.6667 * order[atom][XX] +
777 0.333 * order[atom][YY]));
780 for (slice = 0; slice < nslices; slice++)
782 fprintf(slOrd, "%12d\t", slice);
785 fprintf(slOrd, "%12g\t", distvals[slice][1]); /*use distance value at second carbon*/
787 for (atom = 1; atom < ngrps - 1; atom++)
789 fprintf(slOrd, "%12g\t", slOrder[slice][atom]);
791 fprintf(slOrd, "\n");
797 sprintf(buf, "Orderparameters Sz per atom");
798 ord = xvgropen(afile, buf, "Atom", "S", oenv);
799 fprintf(stderr, "ngrps = %d, nslices = %d", ngrps, nslices);
801 sprintf(buf, "Orderparameters per atom per slice");
802 slOrd = xvgropen(bfile, buf, "Slice", "S", oenv);
804 for (atom = 1; atom < ngrps - 1; atom++)
806 fprintf(ord, "%12d %12g\n", atom, order[atom][ZZ]);
809 for (slice = 0; slice < nslices; slice++)
812 for (atom = 1; atom < ngrps - 1; atom++)
814 S += slOrder[slice][atom];
816 fprintf(slOrd, "%12g %12g\n", slice*slWidth, S/atom);
822 sprintf(buf, "Order tensor diagonal elements");
823 ord = xvgropen(afile, buf, "Atom", "S", oenv);
824 sprintf(buf, "Deuterium order parameters");
825 slOrd = xvgropen(cfile, buf, "Atom", "Scd", oenv);
827 for (atom = 1; atom < ngrps - 1; atom++)
829 fprintf(ord, "%12d %12g %12g %12g\n", atom, order[atom][XX],
830 order[atom][YY], order[atom][ZZ]);
831 fprintf(slOrd, "%12d %12g\n", atom, -1 * (0.6667 * order[atom][XX] +
832 0.333 * order[atom][YY]));
840 void write_bfactors(t_filenm *fnm, int nfile, atom_id *index, atom_id *a, int nslices, int ngrps, real **order, t_topology *top, real **distvals, output_env_t oenv)
842 /*function to write order parameters as B factors in PDB file using
843 first frame of trajectory*/
846 t_trxframe fr, frout;
850 ngrps -= 2; /*we don't have an order parameter for the first or
851 last atom in each chain*/
852 nout = nslices*ngrps;
853 natoms = read_first_frame(oenv, &status, ftp2fn(efTRX, nfile, fnm), &fr,
863 init_t_atoms(&useatoms, nout, TRUE);
866 /*initialize PDBinfo*/
867 for (i = 0; i < useatoms.nr; ++i)
869 useatoms.pdbinfo[i].type = 0;
870 useatoms.pdbinfo[i].occup = 0.0;
871 useatoms.pdbinfo[i].bfac = 0.0;
872 useatoms.pdbinfo[i].bAnisotropic = FALSE;
875 for (j = 0, ctr = 0; j < nslices; j++)
877 for (i = 0; i < ngrps; i++, ctr++)
879 /*iterate along each chain*/
880 useatoms.pdbinfo[ctr].bfac = order[j][i+1];
883 useatoms.pdbinfo[ctr].occup = distvals[j][i+1];
885 copy_rvec(fr.x[a[index[i+1]+j]], frout.x[ctr]);
886 useatoms.atomname[ctr] = top->atoms.atomname[a[index[i+1]+j]];
887 useatoms.atom[ctr] = top->atoms.atom[a[index[i+1]+j]];
888 useatoms.nres = max(useatoms.nres, useatoms.atom[ctr].resind+1);
889 useatoms.resinfo[useatoms.atom[ctr].resind] = top->atoms.resinfo[useatoms.atom[ctr].resind]; /*copy resinfo*/
893 write_sto_conf(opt2fn("-ob", nfile, fnm), "Order parameters", &useatoms, frout.x, NULL, frout.ePBC, frout.box);
896 free_t_atoms(&useatoms, FALSE);
899 int gmx_order(int argc, char *argv[])
901 const char *desc[] = {
902 "[THISMODULE] computes the order parameter per atom for carbon tails. For atom i the",
903 "vector i-1, i+1 is used together with an axis. ",
904 "The index file should contain only the groups to be used for calculations,",
905 "with each group of equivalent carbons along the relevant acyl chain in its own",
906 "group. There should not be any generic groups (like System, Protein) in the index",
907 "file to avoid confusing the program (this is not relevant to tetrahedral order",
908 "parameters however, which only work for water anyway).[PAR]",
909 "[THISMODULE] can also give all",
910 "diagonal elements of the order tensor and even calculate the deuterium",
911 "order parameter Scd (default). If the option [TT]-szonly[tt] is given, only one",
912 "order tensor component (specified by the [TT]-d[tt] option) is given and the",
913 "order parameter per slice is calculated as well. If [TT]-szonly[tt] is not",
914 "selected, all diagonal elements and the deuterium order parameter is",
916 "The tetrahedrality order parameters can be determined",
917 "around an atom. Both angle an distance order parameters are calculated. See",
918 "P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
919 "for more details.[BR]",
923 static int nslices = 1; /* nr of slices defined */
924 static gmx_bool bSzonly = FALSE; /* True if only Sz is wanted */
925 static gmx_bool bUnsat = FALSE; /* True if carbons are unsat. */
926 static const char *normal_axis[] = { NULL, "z", "x", "y", NULL };
927 static gmx_bool permolecule = FALSE; /*compute on a per-molecule basis */
928 static gmx_bool radial = FALSE; /*compute a radial membrane normal */
929 static gmx_bool distcalc = FALSE; /*calculate distance from a reference group */
931 { "-d", FALSE, etENUM, {normal_axis},
932 "Direction of the normal on the membrane" },
933 { "-sl", FALSE, etINT, {&nslices},
934 "Calculate order parameter as function of box length, dividing the box"
935 " into this number of slices." },
936 { "-szonly", FALSE, etBOOL, {&bSzonly},
937 "Only give Sz element of order tensor. (axis can be specified with [TT]-d[tt])" },
938 { "-unsat", FALSE, etBOOL, {&bUnsat},
939 "Calculate order parameters for unsaturated carbons. Note that this can"
940 "not be mixed with normal order parameters." },
941 { "-permolecule", FALSE, etBOOL, {&permolecule},
942 "Compute per-molecule Scd order parameters" },
943 { "-radial", FALSE, etBOOL, {&radial},
944 "Compute a radial membrane normal" },
945 { "-calcdist", FALSE, etBOOL, {&distcalc},
946 "Compute distance from a reference" },
949 rvec *order; /* order par. for each atom */
950 real **slOrder; /* same, per slice */
951 real slWidth = 0.0; /* width of a slice */
952 char **grpname; /* groupnames */
953 int ngrps, /* nr. of groups */
955 axis = 0; /* normal axis */
956 t_topology *top; /* topology */
958 atom_id *index, /* indices for a */
959 *a; /* atom numbers in each group */
960 t_blocka *block; /* data from index file */
961 t_filenm fnm[] = { /* files for g_order */
962 { efTRX, "-f", NULL, ffREAD }, /* trajectory file */
963 { efNDX, "-n", NULL, ffREAD }, /* index file */
964 { efNDX, "-nr", NULL, ffREAD }, /* index for radial axis calculation */
965 { efTPX, NULL, NULL, ffREAD }, /* topology file */
966 { efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
967 { efXVG, "-od", "deuter", ffWRITE }, /* xvgr output file */
968 { efPDB, "-ob", NULL, ffWRITE }, /* write Scd as B factors to PDB if permolecule */
969 { efXVG, "-os", "sliced", ffWRITE }, /* xvgr output file */
970 { efXVG, "-Sg", "sg-ang", ffOPTWR }, /* xvgr output file */
971 { efXVG, "-Sk", "sk-dist", ffOPTWR }, /* xvgr output file */
972 { efXVG, "-Sgsl", "sg-ang-slice", ffOPTWR }, /* xvgr output file */
973 { efXVG, "-Sksl", "sk-dist-slice", ffOPTWR }, /* xvgr output file */
975 gmx_bool bSliced = FALSE; /* True if box is sliced */
976 #define NFILE asize(fnm)
977 real **distvals = NULL;
978 const char *sgfnm, *skfnm, *ndxfnm, *tpsfnm, *trxfnm;
981 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
982 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
988 gmx_fatal(FARGS, "Can not have nslices < 1");
990 sgfnm = opt2fn_null("-Sg", NFILE, fnm);
991 skfnm = opt2fn_null("-Sk", NFILE, fnm);
992 ndxfnm = opt2fn_null("-n", NFILE, fnm);
993 tpsfnm = ftp2fn(efTPX, NFILE, fnm);
994 trxfnm = ftp2fn(efTRX, NFILE, fnm);
997 if (strcmp(normal_axis[0], "x") == 0)
1001 else if (strcmp(normal_axis[0], "y") == 0)
1005 else if (strcmp(normal_axis[0], "z") == 0)
1011 gmx_fatal(FARGS, "Invalid axis, use x, y or z");
1017 fprintf(stderr, "Taking x axis as normal to the membrane\n");
1020 fprintf(stderr, "Taking y axis as normal to the membrane\n");
1023 fprintf(stderr, "Taking z axis as normal to the membrane\n");
1027 /* tetraheder order parameter */
1030 /* If either of theoptions is set we compute both */
1031 sgfnm = opt2fn("-Sg", NFILE, fnm);
1032 skfnm = opt2fn("-Sk", NFILE, fnm);
1033 calc_tetra_order_parm(ndxfnm, tpsfnm, trxfnm, sgfnm, skfnm, nslices, axis,
1034 opt2fn("-Sgsl", NFILE, fnm), opt2fn("-Sksl", NFILE, fnm),
1036 /* view xvgr files */
1037 do_view(oenv, opt2fn("-Sg", NFILE, fnm), NULL);
1038 do_view(oenv, opt2fn("-Sk", NFILE, fnm), NULL);
1041 do_view(oenv, opt2fn("-Sgsl", NFILE, fnm), NULL);
1042 do_view(oenv, opt2fn("-Sksl", NFILE, fnm), NULL);
1047 /* tail order parameter */
1052 fprintf(stderr, "Dividing box in %d slices.\n\n", nslices);
1057 fprintf(stderr, "Only calculating Sz\n");
1061 fprintf(stderr, "Taking carbons as unsaturated!\n");
1064 top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
1066 block = init_index(ftp2fn(efNDX, NFILE, fnm), &grpname);
1067 index = block->index; /* get indices from t_block block */
1068 a = block->a; /* see block.h */
1073 nslices = index[1] - index[0]; /*I think this assumes contiguous lipids in topology*/
1074 fprintf(stderr, "Calculating Scd order parameters for each of %d molecules\n", nslices);
1079 fprintf(stderr, "Calculating radial distances\n");
1082 gmx_fatal(FARGS, "Cannot yet output radial distances without permolecule\n");
1086 /* show atomtypes, to check if index file is correct */
1087 print_types(index, a, ngrps, grpname, top);
1089 calc_order(ftp2fn(efTRX, NFILE, fnm), index, a, &order,
1090 &slOrder, &slWidth, nslices, bSliced, bUnsat,
1091 top, ePBC, ngrps, axis, permolecule, radial, distcalc, opt2fn_null("-nr", NFILE, fnm), &distvals, oenv);
1095 ngrps--; /*don't print the last group--was used for
1096 center-of-mass determination*/
1099 order_plot(order, slOrder, opt2fn("-o", NFILE, fnm), opt2fn("-os", NFILE, fnm),
1100 opt2fn("-od", NFILE, fnm), ngrps, nslices, slWidth, bSzonly, permolecule, distvals, oenv);
1102 if (opt2bSet("-ob", NFILE, fnm))
1107 "Won't write B-factors with averaged order parameters; use -permolecule\n");
1111 write_bfactors(fnm, NFILE, index, a, nslices, ngrps, slOrder, top, distvals, oenv);
1116 do_view(oenv, opt2fn("-o", NFILE, fnm), NULL); /* view xvgr file */
1117 do_view(oenv, opt2fn("-os", NFILE, fnm), NULL); /* view xvgr file */
1118 do_view(oenv, opt2fn("-od", NFILE, fnm), NULL); /* view xvgr file */
1121 if (distvals != NULL)
1123 for (i = 0; i < nslices; ++i)